Vallejos, CA;
Richardson, S;
Marioni, JC;
(2016)
Beyond comparisons of means: understanding changes in gene expression at the single-cell level.
Genome Biology
, 17
(1)
, Article 70. 10.1186/s13059-016-0930-3.
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Abstract
Traditional differential expression tools are limited to detecting changes in overall expression, and fail to uncover the rich information provided by single-cell level data sets. We present a Bayesian hierarchical model that builds upon BASiCS to study changes that lie beyond comparisons of means, incorporating built-in normalization and quantifying technical artifacts by borrowing information from spike-in genes. Using a probabilistic approach, we highlight genes undergoing changes in cell-to-cell heterogeneity but whose overall expression remains unchanged. Control experiments validate our method’s performance and a case study suggests that novel biological insights can be revealed. Our method is implemented in R and available at https://github.com/catavallejos/BASiCS.
| Type: | Article |
|---|---|
| Title: | Beyond comparisons of means: understanding changes in gene expression at the single-cell level |
| Open access status: | An open access version is available from UCL Discovery |
| DOI: | 10.1186/s13059-016-0930-3 |
| Publisher version: | http://doi.org/10.1186/s13059-016-0930-3 |
| Language: | English |
| Additional information: | This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver(http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
| Keywords: | Single-cell RNA-seq, Differential expression, Cellular heterogeneity |
| UCL classification: | UCL UCL > Provost and Vice Provost Offices > UCL BEAMS UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Maths and Physical Sciences |
| URI: | https://discovery.ucl.ac.uk/id/eprint/1555512 |
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